[gmx-users] Doubt in Energy minimization and Position restrained

vivek sharma viveksharma.iitb at gmail.com
Tue Sep 9 11:46:10 CEST 2008

Hi there,

My apologies for asking question from basics.
I have one doubt regarding order of Position restrained and Energy
minimization. While running Position restrained, it soaks water molecule
well within the protein molecule. In doing so on rearranging atoms it will
again raise the energy of system (if I am not wrong). So, do we need to run
Energy minimization again ?
If not, then why ?

With Thanks,
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